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nhansen / SVanalyzer

Tools for the analysis of structural variation in genomes
http://svanalyzer.readthedocs.io/
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Don't hardcode path to `SVcomp.pl` in `SVfindmatches.pl` #1

Closed ifiddes-10x-zz closed 6 years ago

ifiddes-10x-zz commented 6 years ago

https://github.com/nhansen/SVanalyzer/blob/master/scripts/SVfindmatches.pl#L81

nhansen commented 6 years ago

Hi Ian, I've reworked the code for SVanalyzer extensively, and condensed its functionality into five use cases: SVmerge - merge equivalent SVs in one or more VCF files SVcomp - pairs of structural variants (same as previously) SVbenchmark - compare one "test" VCF file to a "truth" VCF file and report precision, recall, f1 SVwiden - characterize structural variants as to similarity at their breakpoints, and thus ambiguity in their positioning SVrefine - call repeat-aware structural variants from assembly alignments (also same as previous versions)

Documentation is at http://svanalyzer.readthedocs.io/en/latest/, and code is considerably cleaner than before. Please give it a try at your convenience!